Genomic Ecology: genes competing for a metabolic niche?

Microbial comparative genomics has undoubtedly cont ributed to the elucidation of fundamental aspects of the genetics, biochemistry a nd evolution of numerous species. A particular important contribution refers to the stu dy of metabolic variability and conservation of enzymatic functions. Since enzymes control almost all biochemical reactions in the metabolism of living organisms, it is extremely important to characterize the genes encoding enzymatic activitie s. The most successful approaches to perform this task are based on sequence similarity searches, using computational tools like BLAST and FASTA. Comparisons of metabolic path ways computationally predicted from completely sequenced genomes of dive rse organisms revealed incomplete or even absent pathways in several analy zed species. In some of these cases, the missing enzymes were substituted by functional equivalent molecules, able to catalyze the same reaction but exhibiting virtually no sequence similarity at the primary level, thus escaping identification by methods base d on sequence similarity. These alternative forms, known as analogous enzymes, aris e from independent evolutionary events, converging for the same biological function , and may be associated with separate phylogenetic lineages and/or possess diffe rent catalytic mechanisms, as well as distinct foldings. Previous works performed by othe r groups suggest that the fraction of enzymatic activities in which multiple events of in dependent origin have occurred may be substantial. However, up to this point, a compre hensive survey of the occurrence, distribution, and implications of these events, com prising fully sequence genomes, has not been done. In addition, an intriguing question ca be raised: since for many enzymes the existence of multiple alternative forms (considering their origins) is true, as well as the pervasiveness of lateral gene transfer between bacterial genomes, one might consider these enzymes as individuals and their clusters as populations, all in competition for a particular metabolic niche? And in such a case, it would be plausible to think that more competitive enzymes would have a s lective advantage over less competitive alternative forms, and would consequent ly spread over diverse bacterial genomes over time? In this work, we investigate the variability and evolution of metabolic pathways in prokaryotes, analyzing the fr equency, distribution and extinction patterns of putative analogous enzymes in the glyco lysis/gluconeogenesis pathway. Acknowledgments We wish to thank Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Programa Estratégico de Apoio à Pesquisa e m Saúde (PAPES), Programa AMSUD-PASTEUR, Red Iberoamericana de Bioinformática (RIB), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Rede Fiocruz, Plataforma de Bioinformática PDTIS, and Fundação de Amparo à Pesq uisa do Estado do Rio de Janeiro (FAPERJ) for their support.